Thermodynamic Driving Forces for Substrate Atom Extraction by Adsorption of Strong Electron Acceptor Molecules

A quantitative structural investigation is reported, aimed at resolving the issue of whether substrate adatoms are incorporated into the monolayers formed by strong molecular electron acceptors deposited onto metallic electrodes. A combination of normal-incidence X-ray standing waves, low-energy electron diffraction, scanning tunnelling microscopy, and X-ray photoelectron spectroscopy measurements demonstrate that the systems TCNQ and F4TCNQ on Ag(100) lie at the boundary between these two possibilities and thus represent ideal model systems with which to study this effect. A room-temperature commensurate phase of adsorbed TCNQ is found not to involve Ag adatoms, but to adopt an inverted bowl configuration, long predicted but not previously identified experimentally. By contrast, a similar phase of adsorbed F4TCNQ does lead to Ag adatom incorporation in the overlayer, the cyano end groups of the molecule being twisted relative to the planar quinoid ring. Density functional theory (DFT) calculations show that this behavior is consistent with the adsorption energetics. Annealing of the commensurate TCNQ overlayer phase leads to an incommensurate phase that does appear to incorporate Ag adatoms. Our results indicate that the inclusion (or exclusion) of metal atoms into the organic monolayers is the result of both thermodynamic and kinetic factors.


Additional experimental results: LEED, SXPS and NIXSW
STM images and LEED patterns recorded from all of the ordered phases of TCNQ and F4-TCNQ on Ag(100) are shown in Figure S1, together with simulations using the LEEDpat program 1 based on the matrices reported in Table S1. The LEED patterns observed from surfaces containing the two coexisting windmill structures (TCNQ:W1 and TCNQ:W2) were complex, as may be expected from the coexistence of two such large unit mesh structures, so no attempt has been made to identify all the observed diffracted beams, but an example of the diffraction pattern is shown in Figure S1. Notice that an unusual feature of the LEED pattern from the F4TCNQ overlayer is the splitting into groups of four spots of all beams with indices comprising one integer and one half-integer, such as (0 ½), (-1 -½) (but not (½ ½)). These beams are circled in Figure S1. The splitting is not reproduced in the simulated pattern using the commensurate matrix 2 Table S1 summarises the main parameters of these different ordered adsorption phases. Note that the numbers of molecules per unit mesh, and hence the area per molecule, are based on the assumption that each elongated bright feature in the STM images corresponds to a molecule.
For the TCNQ:HDI2 phase, this value is somewhat ambiguous; there appear to be three bright features per unit mesh but attributing all of these to TCNQ molecules seems to lead to some unreasonably short intermolecular distances. The STM image also appears to show two rather different types of bright features, one of which shows a brighter circular centre that could, perhaps, be due to the presence of an Ag adatom rather than a TCNQ molecule. Figure S2 shows an STM image recorded from the Ag(100)-TCNQ surface under conditions leading to the formation of islands of the W2 phase, such as that outlined in purple. Notice that S5 the image also shows isolated and linear groups TCNQ 'windmill' structures with bright centres, possibly attributable to Ag adatoms. One such island is outlined in purple.
N 1s and F 1s SXP spectra from the TCNQ:LDC phase on Ag(100), and from the ordered phase of F4TCNQ on Ag(100), which complement the C 1s spectra shown in Figure 2 of the main manuscript, are shown in Figure S3.

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From both surfaces the N 1s spectrum is dominated by a single peak, indicating that all N atoms are in chemically similar bonding sites. The F 1s spectrum does show a second component that is attributed to the effects of radiation damage. F is known to have a particularly high crosssection for electron and photon stimulated desorption, but the presence of this component implies that some F may remain on the surface, possibly in atomic form, rather than being removed into the vacuum.
Chemical-state specific NIXSW measurements of the TCNQ:LDC and TCNQ:HDI1 phases and the ordered phase of F4TCNQ were recorded using the C 1s, N 1s and F 1s photoemission signals as the photon energy was scanned through the normal incidence Ag(200) Bragg reflection condition, as described in the main manuscript. The experimental results and best theoretical fits are shown in Figure S4. The values of the coherent fractions and positions used in these best-fit theory curves for the TCNQ:LDC and F4TCNQ phases (and also from the TCNQ:HCI1 phase) are reported in Table 1 of the main paper.  Table 1 of the main manuscript. Also shown is the reflectivity, R.

Additional DFT structural and energetics results: TCNQ and F4TCNQ on Ag(100)
The results of the DFT structural optimisation for the TCNQ:LDC phase on Ag(100) at the PBE+vdW surf level are shown below in Table S2 together with the experimental values. The results obtained from DFT+MBD-NL calculations of this phase are shown in Table 2 of the main paper. The two computational methods yield very similar results. The results of the structural optimisation for F4TCNQ on Ag(100), with and without Ag adatoms, at the DFT+MBD-NL level are reported in Table 3 of the main paper, while those obtained from similar DFT+vdW surf calculations are shown in Table S3.
unit mesh adopted by F4TCNQ. The results of these calculations are shown in Table S4. in which the molecular windmills are centred around an empty hollow site (see Figure S5(a)) and one in which this hollow site is occupied with an Ag adatom ( Figure S5(b)).   Table S5 compares the adsorption energies of the two structural model. These do indicate an increased stability of the phase in the presence of an adatom, but the magnitude of the energy difference (5 or 6 meV) is very small; indeed, this is significantly less than kT at room temperature (26 meV), which would imply that structures with and without Ag adatoms would S10 be likely to be co-occupied, with similar probability, at room temperature. The failure of these calculations to provide clear support for adatom incorporation in the W2 phase is not particularly surprising. While modelling of an incommensurate phase by a commensurate phase may provide meaningful results on the substrate bonding of well-separated molecules, in a close-packed overlayer, differences in strain and consequential stress could well lead to significant differences in the energetics. Indeed, STM images showing ordered domains of the TCNQ:W2 phase also show isolated TCNQ 'windmills' (also apparently showing central Ag adatoms), as can be seen in Figure S2. This seems to indicate an apparent intrinsic lack of surface stress due to the formation of an ordered 2D array of these features, whereas this is a necessary component of the commensurate DFT-modelled structure. Nevertheless, it is notable that the TCNQ:W2 phase was only observed in coexistence with the TCNQ:LDC and TCNQ:W1 phases. Moreover, the STM images of the TCNQ:W1 phase unit mesh show that it contains four TCNQ in a 'windmill', surrounding a protrusion potentially interpreted as an Ag adatom, but also four additional TCNQ molecules with no evidence if an Ag adatom. It may be, therefore, that the energetic advantage of Ag adatom incorporation may be marginal, even after annealing.